There's a black dragon hidden in the city of Al-Rakkah, the PCs' home town, who has been working to take over the city for centuries. Essentially, he sees the whole city--the bustling trade capital of a vast region, perhaps the entire continent--as his future "hoard." However, he knows he can't just act with impunity, as there are powerful forces in this area that would take him down if he doesn't build up a foundation for his power first. He has slowly, over the course of "generations," built up a financial empire centered around stationery and, as an extension, alchemy--a very lucrative business in a city where mages are hugely important. Having risen to nearly the top of the financial world, he is slowly, slowly putting together a plan to woo the Sultana herself, who's about the same age as the current identity he's using. Her "secret admirer" has made a show of being a huge huge romantic, someone willing to spend on lavish gifts and write genuinely beautiful poetry about her, but he has yet to reveal that it's him sending these gifts.
The party has gotten little, very subtle, hints that there's Something Off about the man, Jafar, and his family. The el-Aly family is notorious for being incredibly reclusive, rarely leaving their personal estates in the city and generally keeping both themselves and their direct family members out of the spotlight, despite having been (for about three generations now) some of the wealthiest people in town. They also tend to completely disappear from public life after passing the fortune on to the "next generation." Further, the party knows that the first ancestor of the el-Aly family arrived by boat from Elsewhere a couple centuries ago--precisely when the black dragon is thought to have arrived.
Again, the whole point here is that I want this to be subtle as heck. My ideal situation is that the party either doesn't figure it out until Jafar reveals his true nature, or that they figure it out only a little bit before his intended reveal. The former has maximum drama points, while the latter will give the players a sense of immense satisfaction at being able to foil a big bad's plan in advance. I obviously am not going to FORCE either of those situations to happen, because I genuinely want my players to have a fair shot at figuring this out for themselves. But Jafar has spent a long time getting very good at concealing his identity. He has some "chronic PC underestimation" problems, but other than that, he covers his tracks well. If the party really does figure it out and surprise him, awesome; otherwise, I look forward to them saying,"...God, we SHOULD have known it was him all along, shouldn't we?"